New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
21 months
263
12
86362
7391
Parser of scientific names (...) !
Dmitry Mozzherin
6 months
18
5
45633
4866
0
0
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
6 weeks
5
1
39689
3187
0
3
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
9 months
14
11
36437
3537
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
3 days
17
6
34051
5773
6
12
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
3 days
2
...
28098
2103
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
11 months
13
1
23694
2658
0
0
Http requests to entrez e-utilities (...)
Jared Ning
3 years
4
...
22838
2187
0
0
Gadgets for bioinformatics (...)
Shintaro Katayama
21 months
...
22828
3410
0
0
A Ruby api for interacting with biomart services (...) !
Darren Oakley
3 years
17
4
22250
1568
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
11 months
21601
1564
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
11 weeks
55
28
19695
2283
8
200
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
17950
1544
0
0
Create pretty svg-format images of features, gene models (...)
Dan MacLean
13 months
9
5
17770
4129
0
0
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
31
17019
2127
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
1
...
15231
1222
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
14731
1860
0
0
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
14280
1481
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
3 months
12
...
13604
2230
0
0
A simple obo file handler (...) !
mjy
3 years
4
...
13331
982
0
0
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
10641
1079
0
0
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
9 months
7
5
10458
1186
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
9 months
8
20
10263
1398
0
0
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
7 weeks
11
2
9724
2464
0
10
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
2 years
1
...
9000
954
0
0
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
2
1
8958
768
0
0
Data mining algorithms for jRuby (...)
arrigonialberto86
17 months
14
3
8850
1697
0
0
Low memory sequence emitters (...)
Pjotr Prins
9 months
8
1
8568
934
0
0
A nexus file format (phylogenetic inference) parser in (...) !
mjy
3 years
1
...
8529
533
0
0
Build genome output files (...)
Michael Barton
18 months
5
...
8093
560
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
6 months
1
...
8014
957
0
0
Ruby support for the baclava file format (...) !
Robert Haines
12 months
1
...
7956
476
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
7834
617
0
0
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
7688
509
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
7527
776
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
20 months
8
...
7377
712
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
2
7342
635
0
0
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
21 months
5
...
7230
920
0
0
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
7207
688
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
7193
781
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
3 years
3
...
7153
642
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
11 months
...
7124
597
0
0
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
6687
482
0
0
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
6572
555
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
6277
498
0
0
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5971
460
0
0
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
2 weeks
2
1
5887
2582
0
13
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
5575
715
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
5285
471
0
0
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
9
...
5223
418
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
19 months
11
2
5086
1027
0
0
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
5082
477
0
0
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
4883
479
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
22 months
2
1
4817
621
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
38
5
4768
247
0
0
Ruby binding for samtools tabix (...)
throwern
17 months
3
...
4554
622
0
0
Taverna player is a rails plugin to run (...)
Robert Haines
2 days
4
3
4361
1001
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
4066
471
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
4011
484
0
0
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
4001
311
0
0
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
3984
471
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
3978
459
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
3967
313
0
0
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3730
338
0
0
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
3699
350
Parser to work with file formats used in (...)
Ben J Woodcroft
7 weeks
...
3658
1388
0
8
Fast multi-threaded vcf parser (...)
Pjotr Prins
9 weeks
15
7
3544
1431
0
83
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3444
307
0
0
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
17 months
3336
634
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
3273
318
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3228
320
0
0
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
2 years
3202
461
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
21 months
...
3086
472
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
18 months
1
...
3074
471
0
0
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2893
323
0
0
A protparam compatible utility for BioRuby (...)
hryk
2 years
1
...
2826
312
0
0
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
2731
313
0
0
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
4 months
...
2564
1156
0
0
Publish scientific results to the semantic web (...) !
Will Strinz
8 months
3
16
2449
383
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
11 months
1
...
2179
621
0
0
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2071
144
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
2066
165
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
2062
166
0
0
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
5 years
1
...
1987
153
0
0
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
12 months
6
...
1918
180
0
0
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1803
154
0
0
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1792
149
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1769
158
0
0
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1768
169
0
0
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
7 weeks
1
1763
992
0
9
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1748
161
0
0
Gggenome Ruby client (...)
Mitsuteru Nakao
18 months
1
...
1746
310
0
0
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1735
160
0
0
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1719
155
0
0
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1697
159
0
0
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1684
166
Ruby ensembl rest api (...)
Alberto Donizetti
17 months
3
1
1665
311
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1655
148
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1652
157
0
0
A general purpose framework for scripted handling of (...) development/stable
mjy
23 months
2
...
1628
169
0
0
Generalized linear models for statsample (...)
Ankur Goel
17 months
1610
308
Biostars data-mining and statistical analysis (...)
Joachim Baran
10 months
1594
476
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1563
172
0
0
Build graph with jRuby (...)
Matteo Picciolini
2 years
1464
168
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
1
...
1449
157
0
0
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
1
...
1433
104
0
0
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
3 months
...
1408
737
0
0
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
13 months
...
1357
313
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
13 months
...
1343
321
Bio-repeatmasker (...)
Andrei Rozanski
13 months
1319
310
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1204
159
0
0
A parser for cigar format alignments (...)
Ben J Woodcroft
12 months
4
...
1183
322
0
0
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
5 years
5
...
1181
377
Web server for bio-samtools (...)
homonecloco
9 months
...
1040
324
0
0
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
20 months
2
...
994
166
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
19 months
...
931
160
0
0
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
4 months
836
334
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
90
1
603
205
0
0
Mine publications for gene names (...)
Pjotr Prins
12 months
...
602
165
0
0
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
11 months
540
189
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
10 weeks
1
...
505
505
0
11
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
7 months
...
449
171
0
1
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
5 months
...
396
198
0
0
(...) pre
pre
395
25
!
Rocker (...) new
Luis (Coto) Orellana, Luis M. Rodriguez-R
5 weeks
379
379
Tools to work with fasta files, indexed with (...)
homonecloco
4 months
...
363
184
0
0
Tools to manipulate blat files from the command (...)
homonecloco
4 months
...
356
172
0
0
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
309
100
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
3 months
...
303
184
0
0
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
3 months
...
296
177
0
0
!
Helper methods for reading .delta files (...) new
robsyme
2 weeks
...
144
144
0
11
(...) pre
pre
140
33
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-03-01
**) number of commits on GitHub (last 7 days & last 90 days)